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humlab-sead / sead_clearinghouse_import

Temporary import system for SEAD Clearinghouse
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Dendro Build: Errors in import file #15

Closed roger-mahler closed 4 years ago

roger-mahler commented 4 years ago 
WARNING tbl_sample_group_coordinates has EXTRA DATA columns: sample_group_name
WARNING tbl_sample_group_description_type_sampling_contexts has EXTRA DATA columns: type name
WARNING! Duplicate check of tbl_site_references.system_id failed
CRITICAL ERROR tbl_sample_group_descriptions has NO DATA!
CRITICAL ERROR tbl_site_references has missing system id values
CRITICAL ERROR tbl_sites has missing system id values

ABORTED CRITICAL ERROR dendro_build_data_latest_20191213 
Process ABORTED since submission does not conform to SPECIFICATION
roger-mahler commented 4 years ago

CRITICAL ERROR tbl_sample_group_descriptions has NO DATA! => alias removed from meta CRITICAL ERROR tbl_site_references has missing system id values => empty rows removed ???? CRITICAL ERROR tbl_sites has missing system id values => empty rows removed ????

roger-mahler commented 4 years ago 
Processing tbl_abundances...
Table tbl_abundances, id=1, process failed for column taxon_id
CRITICAL FAILURE: Table tbl_abundances 'DataFrame' object has no attribute 'system_id'
CRITICAL ERROR
Traceback (most recent call last):
  File "importer\xml_processor.py", line 136, in process_data
    fk_data_row = fk_data_table.loc[(fk_data_table.system_id == fk_system_id)]
AttributeError: 'DataFrame' object has no attribute 'system_id'

ABORTED CRITICAL ERROR dendro_build_data_latest_20191213
Traceback (most recent call last):
  File "importer\process.py", line 92, in process
    option.xml_filename = self.process_excel_to_xml(option, basename, timestamp)
  File "importer\process.py", line 49, in process_excel_to_xml
    service.process(submission, option.table_names)
  File "importer\xml_processor.py", line 218, in process
    self.process_data(submission, data_tablenames)
  File "importer\xml_processor.py", line 136, in process_data
    fk_data_row = fk_data_table.loc[(fk_data_table.system_id == fk_system_id)]
AttributeError: 'DataFrame' object has no attribute 'system_id'
(sead_clearinghouse_import)
roger-mahler commented 4 years ago

Table taxa_tree_masteris missing column system_id. I guess this is new records?

roger-mahler commented 4 years ago

Fixed